Closed jrobinso closed 2 years ago
For progress on VCF exports, see in-progress issue: https://github.com/griffithlab/civicpy/issues/3
Thanks @ahwagner . BTW, I can't seem to apply a label (hackathon). Perhaps I don't have the right premissions?
No, it looks as though labels are one of those things that requires a team member to set (https://help.github.com/articles/repository-permission-levels-for-an-organization/). Thanks for the heads-up, adding the hackathon label now.
Integrate the CIViC DB with genome browsers including igv.js, JBrowse, and possibly IGV. This integration could take 2 forms, not mutually exclusive
(1) Link out to CIViC from VCF and other variant track types (e.g. SnpDB) and provide variant details in a popup.
(2) When zoomed in to “gene” level, query the CIViC API for variants as genes come into view and display as a track. Clicking on a variant would query the API and bring up details in a popup.
The motivation is to give researchers browsing their own variants in the genome browser easy access to CIViC data. igv.js does a similar thing now with Cravat.
If there is interest in this proposal I could outline an implementation approach here, or save it for the hackathon.